Lygos, Inc. Employee Handbook - a draft

I) Introduction


Lygos harnesses biological processes to convert low-cost sugar and other abundant substrates into high-value chemicals. We target chemicals where biological production is lower cost than existing, petroleum processes. Our processes decrease greenhouse gases and eliminate use of toxic catalysts.



Our values are



Our current goals are


II) Employment Policies

At-Will Employment

While we sincerely hope that your employment here at Lygos will be a positive and rewarding experience, we cannot, for legal reasons, make any guarantees about your continued employment. Your employment here is at will. This means that you are free to quit at any time, for any reason, just as we are free to terminate your employment at any time, for any reason with or without notice, with or without cause. Nothing in this Handbook constitutes a contract or promise of continued employment.


Equal Opportunity Employment

Lygos is an Equal Opportunity Employer. The company supports diversity and inclusion in its core values and does not discriminate against qualified employees or applicants because of race, color, religion, gender identity, sex, sexual preference, sexual identity, pregnancy, national origin, ancestry, citizenship, age, marital status, physical disability, mental disability, medical condition, military status, or any other characteristic protected by federal or state law or local ordinance. When necessary, the company will reasonably accommodate employees and applicants with disabilities if the person is otherwise qualified to safely perform all of the essential functions of the position.


Code of Conduct

Lygos is dedicated to creating an inclusive environment for everyone, regardless of race, ethnicity, nationality, religion, color, sex (with or without sexual conduct and including pregnancy and sexual orientation involving transgender status/gender identity, and sex-stereotyping), national origin, age, disability (physical or mental), genetic information, sexual orientation, gender identity, parental status, marital status, and political affiliation as well as gender expression, mental illness, socioeconomic status or background, neuro(a)typicality, physical appearance, body size, computing experience, or clothing. Consider that calling attention to differences can feel alienating.

We do not tolerate harassment of community members in any form. Harassment includes offensive verbal comments related to the protected classes above, sexual images in public spaces, deliberate intimidation, stalking, following, photography or audio/video recording against reasonable consent, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention. Harassment does not need to be recognized as unwanted or unwelcome by anyone other than the person being harassed.

Be careful in the words that you choose. Remember that sexist, racist, and other exclusionary jokes can be offensive to those around you. Offensive jokes are not appropriate and will not be tolerated under any circumstance.

Participants asked to stop any harassing behavior are expected to comply immediately. If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Eric Steen, Jeffrey Dietrich, Johan van Walsem, or Nick Ohler immediately.


Sexual Harassment Policy

Defining Sexual Harassment

"Sexual harassment" is unwelcome conduct of a sexual nature that is sufficiently persistent or offensive to unreasonably interfere with an employee's job performance or create an intimidating, hostile or offensive working environment. Sexual harassment is defined by the Equal Employment Opportunity Commission Guidelines as unwelcome sexual advances, requests for sexual favors and other verbal or physical conduct of a sexual nature when, for example: a) submission to such conduct is made either explicitly or implicitly a term or condition of an individual's employment, b) submission to or rejection of such conduct by an individual is used as the basis for employment decisions affecting such individual, or c) such conduct has the purpose or effect of unreasonably interfering with an individual's work performance or creating an intimidating, hostile or offensive working environment.

Under Title VII of the Civil Rights Act of 1964, there are two types of sexual harassment: a) quid pro quo and 2) hostile work environment. Sexual harassment can be physical and psychological in nature. An aggregation of a series of incidents can constitute sexual harassment even if one of the incidents considered on its own would not be harassing. Employees are prohibited from harassing other employees whether or not the incidents of harassment occur on employer premises and whether or not the incidents occur during working hours.

Examples of Prohibited Conduct

Though sexual harassment encompasses a wide range of conduct, some examples of specifically prohibited conduct include the following:

  • Physical assaults of a sexual nature, such as rape, sexual battery, molestation or attempts to commit these assaults, and intentional physical conduct that is sexual in nature, such as touching, pinching, patting, grabbing, brushing against another employee's body or poking another employee's body
  • Unwelcome sexual advances, propositions or other sexual comments, such as sexually oriented gestures, noises, remarks, jokes or comments about a person's sexuality or sexual experience
  • Preferential treatment or promises of preferential treatment to an employee for submitting to sexual conduct, including soliciting or attempting to solicit any employee to engage in sexual activity for compensation or reward
  • Subjecting, or threats of subjecting, an employee to unwelcome sexual attention or conduct or intentionally making performance of the employee's job more difficult because of that employee's sex
  • Sexual or discriminatory displays or publications anywhere in Lygos’ workplace by the Lygos employees
  • Retaliation for sexual harassment complaints

Responding to Conduct in Violation of Policy


If an employee believes that he or she has been subject to sexual harassment or any unwelcome sexual attention, he or she may address the situation directly and immediately to the harasser, if possible. If the inappropriate conduct does not cease, or if the employee is unable to or uncomfortable with addressing the alleged harasser directly, he or she should report the incident to their own manager, directly to Eric Steen, Jeffrey Dietrich, Johan van Walsem, or Nick Ohler, or to the Human Resources (HR officer). It is helpful to record of the date, time and nature of the incident(s) and the names of any witnesses. It is important to report any and all concerns of sexual harassment or inappropriate sexual conduct as soon as possible. Management must be made aware of the situation so that it can conduct an immediate and impartial investigation and take appropriate action to remediate or prevent the prohibited conduct from continuing.


Managers must deal expeditiously and fairly with allegations of sexual harassment within their departments whether or not there has been a written or verbal complaint. They must:

  • Take all complaints or concerns of alleged or possible harassment or discrimination seriously no matter how minor or who is involved
  • Ensure that harassment or inappropriate sexually oriented conduct is immediately reported to the HR officer so that a prompt investigation can occur
  • Take any appropriate action to prevent retaliation or prohibited conduct from recurring during and after any investigations or complaints

Managers who knowingly allow or tolerate sexual harassment or retaliation, including the failure to immediately report such misconduct to the HR officer, are in violation of this policy and subject to discipline.

Human Resources

The HR officer is responsible for:

  1. Ensuring that both the individual filing the complaint (hereafter referred to as the "complainant") and the accused individual (hereafter referred to as the "respondent") are aware of the seriousness of a sexual harassment complaint.
  2. Explaining Lygos' sexual harassment policy and investigation procedures to the complainant and the respondent.
  3. Exploring informal means of resolving sexual harassment complaints.
  4. Notifying the police if criminal activities are alleged.
  5. Arranging for an investigation of the alleged harassment and the preparation of a written report.
  6. Submitting a written report summarizing the results of the investigation and making recommendations to designated company officials.
  7. Notifying the complainant and the respondent of the corrective actions to be taken, if any, and administering those actions.

Complaint Resolution Procedures

Individuals should report complaints of conduct believed to violate Lygos' sexual harassment policy according to the policy's complaint procedures. To initiate a formal investigation into an alleged violation of this policy, employees may be asked to provide a written statement about the alleged misconduct to the HR officer. Complaints should be submitted as soon as possible after an incident has occurred. The HR officer may assist the complainant in completing the statement.

To ensure the prompt and thorough investigation of a sexual harassment complaint, the complainant should provide as much of the following information as is possible:

  1. The name, department and position of the person or persons allegedly causing the harassment.
  2. A description of the incident(s), including the date(s), location(s) and the presence of any witnesses.
  3. The effect of the incident(s) on the complainant's ability to perform his or her job, or on other terms or conditions of his or her employment.
  4. The names of other individuals who might have been subject to the same or similar harassment.
  5. What, if any, steps the complainant has taken to try to stop the harassment.
  6. Any other information the complainant believes to be relevant to the harassment complaint.


Employees who violate this policy are subject to appropriate discipline. If an investigation results in a finding that this policy has been violated, the mandatory minimum discipline is a written reprimand. The discipline for very serious or repeat violations is termination of employment. Persons who violate this policy may also be subject to civil damages or criminal penalties.


All inquiries, complaints and investigations are treated confidentially. Information is revealed strictly on a need-to-know basis. Information contained in a formal complaint is kept as confidential as possible. However, the identity of the complainant is usually revealed to the respondent and witnesses. The HR officer takes adequate steps to ensure that the complainant is protected from retaliation during the period of the investigation. All information pertaining to a sexual harassment complaint or investigation is maintained by the HR officer in secure files. The HR officer can answer any questions relating to the procedures for handling information related to sexual harassment complaints and investigations to complainants and respondents.

Other Available Procedures

The procedures available under this policy do not preempt or supersede any legal procedures or remedies otherwise available to a victim of sexual harassment under local, state or federal law.



Paychecks issued every two weeks Fridays. You can access payroll information by logging into your Paychex account. You were assigned a Paychex account on your first day. Please contact Ann Nguyen for additional information.


III) Benefits and Perks

Office Perks


Snacks, coffee, and tea are provided in the kitchen.


Responsible Vacation Policy

We all work hard, and we recognize that! In order to give our best and live a well-balanced life, we need to take time off to pursue interests outside of work, whether that means sitting on a beach or climbing a mountain. At Lygos, we believes you should take responsibility for managing your own time, communication, and collaboration with your team. To that end, we adopted a responsible vacation policy that gives each full-time employee the flexibility to take planned vacations as needed.

  • Instead of accruing vacation time, you plan the vacation time you would like to take with your manager
  • Ensure time away is taken into account for project planning
  • Create a Vacation event on the Lygos Corporate Calendar
  • Since employees don't "accrue" vacation days under this policy, you will not receive compensation for "unused" vacation time if/when you leave Lygos
  • You will continue to have full Lygos benefits through vacation periods, and your equity will continue to vest to the fullest extent permitted by governing plans and agreements

Vacation under this policy is intended to build trust in working relationships. Lygos expects that employees will use good judgement, take time off in appropriate amounts, and coordinate with their managers in advance, while completing their workloads. If an employee's performance declines due to abuse of this policy, Lygos reserves the right to review the employee's use of this policy and determine if discipline or termination is appropriate.

Company Holidays

  • New Year's Day (1/1)
  • President's Day (2/19)
  • Memorial Day (Last Monday of May)
  • Independence Day (7/4)
  • Labor Day (First Monday of September)
  • Veteran's Day (11/12)
  • Thanksgiving (Fourth Thursday of November)
  • Friday after Thanksgiving (Fourth Friday of November)
  • Christmas (12/25)

If a holiday falls on a weekend, the weekday before or after the holiday is generally observed. Each team should decide what needs to be accomplished during these holidays to ensure all needs are met.


Education Benefit Program

Lygos encourages employees to pursue additional formal education to enhance their knowledge and skills. In order to do that, we've created an education benefit program that allows you to grow and learn at the company's expense.

  • Each employee has $1,000 to be used annually in classes, conferences, travel, and books to benefit career growth while at Lygos
  • The minimum eligibility is six months of company service
  • An employment year is based on the employee's anniversary
  • Non-limiting example uses include career development classes, technical training workshops, professional study courses, professional exams conferences, travel and accommodations for classes and conferences, and educational books
  • To participate, a request is made to the manager for approval on a case-by-case basis
  • The employee may be reimbursed for expenses after approval is received from the manager
  • At the conclusion of the education activity or purchase, the employee must provide a receipt, transcript, certification of completion, or other document to the HR officer


Medical Benefits and Policies

Medical, Vision and Dental Insurance

Lygos provides medical, vision and dental benefits for all full-time staff members (40 hours) and their families. Please contact Ann Nguyen if you have any coverage questions.

Workers' Comp

We provide workers' compensation insurance for qualifying injuries "on the job" for partial loss of wages and medical expenses, for employees on Lygos payroll. We don't determine what qualifies - the insurer does, based on state regulations. Please report any injuries to your manager as soon as possible and no later than 24 hours after an accident or injury has occurred in order to meet the requirements of our insurer. General information about workers' compensation in California can be found here.

State Disability

Staff members who become disabled and unable to perform the functions of their job may be eligible to apply for State Disability Insurance to receive partial income. This income will be coordinated with eligible Lygos benefits, which may include Sick Leave Policy and Caretaker Leave Policy. More information on California State Disability can be found here.


Sick Leave Policy

Lygos offers unlimited sick days. All sick days should be entered as a Sick Event on the Lygos Corporate Calendar. Get the rest you need, and don't get the whole company sick.

  • Sick leave may be used for purposes that extend beyond your own sickness but don't rise to the level of a serious health condition
  • Sick days may be used to care for yourself or a family member (which includes a spouse or domestic partner, parent, parent--in-law, sibling, grandparent, or grandchild); for employees who do not have a spouse or domestic partner, the employee may designate an alternative person for whom the employee may use paid sick leave to provide care
  • An employee who is a victim of domestic assault, sexual violence, or walking may also use sick days for certain purposes related to the domestic assault, sexual violence, or stalking, including seeking legal relief; ensuring the health, safety, or welfare of the employee or children; or obtaining specified services or consulting
  • If you need extended time off (more than 5 consecutive business days) for illness or injury, your manager will need to evaluate the absence request and the HR officer will determine whether the absence will be approved and/or qualify for a leave of absence of the law


Caretaker Leave Policy

Lygos offers a 100% paid caretaker/parental leave policy for up to 16 weeks per calendar year for employee and absence that meet the requirements set forth in this policy.

  • Leave may be taken for the birth, adoption, or foster placement of a child; caring for an employee's spouse, domestic partner, child, or parent with a serious health condition; or the serious health condition the the employee
  • The pay benefit during the caretaker leave is coordinated with state disability and paid family leave benefits, in addition to any other wage substitution benefits for which the employee is eligible
  • Upon return from a leave, employees will generally be reinstate to their original or a comparable position and salary
  • Employees on leave will continue to be eligible to participate in company-sponsored benefits, including equity vesting and health insurance, to the fullest extent permitted by the governing plans and agreements
  • Caretaker leave, vacation time, and sick leave do not overlap and must be approved separately


  • Requests for leaves must be submitted in writing to the manager at least 30 days prior to the commencement of the leave, although additional notice is encouraged and appreciated
  • To be eligible for paid caretaker leave, the employee must have been employed with Lygos at least 6 months; employees not meeting this eligibility requirement may take up to 12 weeks of unpaid leave for an absence that would otherwise qualify for leave under this policy
  • Employees will coordinate with Ann Nguyen on filing paperwork with CA SDI
  • Leave taken in connection with the birth, adoption, or foster placement of a child must be completed within one year of the birth, adoption, or placement giving rise to the leave entitlement

Scenarios of Caretaker Leave

Sick family member leave for four weeks

  • An employee has a need to take care of a relative/parent/etc and requests four weeks of leave
  • The leave is immediate and sudden
  • Lygos covers Week 1 at 100% of salary during waiting period
  • If approved, CA Paid Family Leave covers up to 55% of salary and Lygos covers 45% (plus any shortfall) of salary for weeks 2-4

Pregnancy disability/bonding leave for 16 weeks

  • An employee is pregnant and requests leave of 16 weeks in connection with birth and bonding with the baby
  • Medical certification supports leave starting four weeks before due date
  • State Disability Insurance benefits apply to pregnancy disability; Paid Family Leave benefits apply to baby bonding
  • Lygos covers Week 1 at 100% during waiting period
  • CA State Disability Insurance covers up to 55% and Lygos covers 45% (plus any shortfall) for Weeks 2-4 before birth
  • CA State Disability Insurance covers up to 55% and Lygos covers 45% (plus any shortfall) for Weeks 1-6 after birth
  • CA Family Paid Leave covers up to 55% and Lygos covers 45% (plus any shortfall) for Weeks 7-16 after birth

Parental leave for 16 weeks

  • An employee's partner gives birth or employee adopts a child and employee requests leave of 16 Weeks to bond with the child
  • Lygos covers Week 1 at 100% of salary during waiting period
  • CA Paid Family Leave CA covers up to 55% and Lygos covers 45% (plus any shortfall) for Weeks 2-7 after birth/adoption

All of the above are example scenarios given real world situations and assume that the requesting employee. meets eligibility requirements. If any complications or unplanned scenarios arise, please communicate and coordinate with your manager and Ann Nguyen.


Other Types of Leaves

Bereavement Leave

Lygos offers 3 paid days off per year for the loss of a loved one. Please coordinate your needed time with Ann Nguyen.

Witness and Jury Duty

Witness and jury duty leave allow employees to fulfill their civic responsibilities by serving as jurors and subpoenaed witnesses up to 10 paid working days per calendar year. During that period, employees will receive the difference between their regular base pay and any payment received for their court duties. Witness and jury duty leave beyond 10 days will be unpaid, except as required by law.

Unpaid Leave

Lygos may grant unpaid leave from time to time in extraordinary circumstances. If you need unpaid leave, please discuss with your manager.


401(k) Plan

Lygos offers a voluntary pre-tax salary reduction plan in which full-time employees may elect to participate in. Further details about the plan may be obtained from Ann Nguyen.


IV) Processes and Practices

Recurring Meetings

Whole Company

All Hands (Monthly, Wednesday, 3.30 to 5 p.m.)

Each department gives overview of the month's activities.

Department Meetings

Weekly (meeting time determined by individual departments)

Technical staff discuss goals, milestones, weekly activities, and project updates, which include troubleshooting, brainstorming, allocation of resources, and gripes.



Each employee meets regularly with their managers talk through what they're doing and what they need.


Remote Work

There are varying levels of remoteness that should be treated with increasing levels of care. In general, the more remote you are, the more preparation, forewarning, and effort should be put into it.

Occasional home or coffee shop work

  • Notify manager and the team before day-of working remotely, where you'll be and when, and how to reach you
  • Create a Working Remotely event on the Lygos Corporate Calendar

Occasional remote trips; 2 days or more

  • Requires manager approval
  • Notify manager and the team at least several days before you leave; ideally, once the trip is booked and again a few days before departure
  • Notify manager and the team where you'll be and when, and how to reach you
  • Ensure time away is taken into account for project planning
  • Create a Working Remotely event on the Lygos Corporate Calendar

Regular remote segments

  • Requires manager approval and training
  • Notify manager and the team where you'll be and when, and how to reach you
  • Ensure time away is taken into account for project planning
  • Create a Working Remotely event on the Lygos Corporate Calendar